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- PDB-6vhq: Crystal structure of Bacillus subtilis levansucrase (D86A/E342A) ... -

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Basic information

Entry
Database: PDB / ID: 6vhq
TitleCrystal structure of Bacillus subtilis levansucrase (D86A/E342A) in complex with oligosaccharides
ComponentsGlycoside hydrolase family 68 protein
KeywordsTRANSFERASE / Levansucrase / Glycoside hydrolase / Levan / Fructose polymers
Function / homology
Function and homology information


levansucrase / levansucrase activity / carbohydrate utilization / extracellular region
Similarity search - Function
Glycoside hydrolase, family 68 / Levansucrase/Invertase / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily
Similarity search - Domain/homology
levanbiose / BROMIDE ION / Levansucrase / Levansucrase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.047 Å
AuthorsDiaz-Vilchis, A. / Raga-Carbajal, E. / Rojas-Trejo, S. / Olvera, C. / Rudino-Pinera, E.
Funding support Mexico, 3items
OrganizationGrant numberCountry
Other governmentConsejo Nacional de Ciencia y Tecnologia-CB-2013-219728 Mexico
Other governmentConsejo Nacional de Ciencia y Tecnologia-BMBF-2015-267620 Mexico
Other governmentUniversidad Nacional Autonoma de Mexico-PAPIIT IN213616 Mexico
CitationJournal: J.Biol.Chem. / Year: 2020
Title: The molecular basis of the nonprocessive elongation mechanism in levansucrases.
Authors: Raga-Carbajal, E. / Diaz-Vilchis, A. / Rojas-Trejo, S.P. / Rudino-Pinera, E. / Olvera, C.
History
DepositionJan 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside hydrolase family 68 protein
B: Glycoside hydrolase family 68 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,83617
Polymers104,7222
Non-polymers4,11415
Water9,728540
1
A: Glycoside hydrolase family 68 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,86210
Polymers52,3611
Non-polymers2,5019
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycoside hydrolase family 68 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9747
Polymers52,3611
Non-polymers1,6136
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.313, 78.665, 78.732
Angle α, β, γ (deg.)90.000, 93.940, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glycoside hydrolase family 68 protein / Levansucrase


Mass: 52360.797 Da / Num. of mol.: 2 / Mutation: D86A, E342A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Gene: sacB, B4417_3269, ETA10_18085, ETL41_09350, FVD40_16900
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0PFL2, UniProt: P05655*PLUS

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Sugars , 2 types, 4 molecules

#2: Polysaccharide beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D- ...beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose


Type: oligosaccharide / Mass: 990.860 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DFrufb2-6DFrufb2-6DFrufb2-6DFrufb2-6DFrufb2-6DFrufb2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[ha122h-2b_2-5]/1-1-1-1-1-1/a6-b2_b6-c2_c6-d2_d6-e2_e6-f2WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(6+2)][b-D-Fruf]{[(6+2)][b-D-Fruf]{[(6+2)][b-D-Fruf]{[(6+2)][b-D-Fruf]{[(6+2)][b-D-Fruf]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-fructofuranose-(2-6)-beta-D-fructofuranose / levanbiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: levanbiose
DescriptorTypeProgram
DFrufb2-6DFrufb2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[ha122h-2b_2-5]/1-1/a6-b2WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(6+2)][b-D-6-deoxy-Fruf]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 551 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Br / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 540 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Nonpolymer detailsThe entry contains the oligosaccharide levanhexaose, a 6 fructose units bound by beta2-6 glycosidic bonds

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.22 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 6 / Details: 30 % w/v PEG 2000 MME and 150 mM Potassium Bromide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.047→35.205 Å / Num. obs: 53175 / % possible obs: 99.99 % / Observed criterion σ(I): 3.5 / Redundancy: 2.7 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 23.9
Reflection shellResolution: 2.047→2.09 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 5145 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OYG

1oyg


Resolution: 2.047→35.205 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.23
RfactorNum. reflection% reflection
Rfree0.2348 2606 4.93 %
Rwork0.1672 --
obs0.1704 52881 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.72 Å2 / Biso mean: 28.2683 Å2 / Biso min: 7.12 Å2
Refinement stepCycle: final / Resolution: 2.047→35.205 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6968 0 234 540 7742
Biso mean--46.55 33.53 -
Num. residues----880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0167509
X-RAY DIFFRACTIONf_angle_d1.47610195
X-RAY DIFFRACTIONf_chiral_restr0.0761130
X-RAY DIFFRACTIONf_plane_restr0.0081287
X-RAY DIFFRACTIONf_dihedral_angle_d15.1064320
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0471-2.08430.29721380.2057247794
2.0843-2.12440.26071260.19982707100
2.1244-2.16770.28481290.18742635100
2.1677-2.21490.25991230.18192634100
2.2149-2.26640.2481300.18622676100
2.2664-2.3230.2841420.18552665100
2.323-2.38580.26061590.1772647100
2.3858-2.4560.31011520.18432620100
2.456-2.53530.2721280.18282683100
2.5353-2.62590.27181360.1622642100
2.6259-2.7310.24921570.16292624100
2.731-2.85520.2211410.1692661100
2.8552-3.00570.25841150.16842684100
3.0057-3.19390.22141370.17052657100
3.1939-3.44030.23021590.1779255597
3.4403-3.78610.22261540.1548261899
3.7861-4.33310.20231050.1452266998
4.3331-5.4560.17231370.13782676100
5.456-35.21050.23071380.1828274599

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